Minor improvements

- added requirements file
- minor reformat

ORIGAMI_ANALYSE/origami/ORIGAMI.py

@@ -17,20 +17,31 @@
 # -------------------------------------------------------------------------
 # __author__ lukasz.g.migas
 
+import warnings
+from copy import deepcopy
+
 # Import libraries
-import wx, os, sys, time, re, gc, path, threading, random, webbrowser
+import gc
 import numpy as np
+import os
+import pandas as pd
+# import path
+import random
+import re
+import sys
+import threading
+import time
+import webbrowser
+import wx
+import wx.lib.agw.multidirdialog as MDD
 from _codecs import encode
-from numpy.ma import masked_array # @UnresolvedImport
+from math import sqrt, log
+from numpy.ma import masked_array  # @UnresolvedImport
+from scipy.stats import linregress  # @UnresolvedImport
 from wx.lib.pubsub import setuparg1
-import wx.lib.agw.multidirdialog as MDD
-from copy import deepcopy
-import pandas as pd
+
 from ids import *
-from math import sqrt, log
-from scipy.stats import linregress # @UnresolvedImport
 
-import warnings
 # needed to avoid annoying warnings to be printed on console
 warnings.filterwarnings("ignore",category=DeprecationWarning)
 warnings.filterwarnings("ignore",category=RuntimeWarning)

ORIGAMI_ANALYSE/origami/config.py

@@ -41,7 +41,7 @@ def __init__(self):
         self.loggingFile_path = None
 
         self.document_version = "19-10-2018"
-        self.version = "1.2.0.4"
+        self.version = "1.2.1.5"
         self.unidec_engine = None
         self.links = {
             'home' : 'https://www.click2go.umip.com/i/s_w/ORIGAMI.html',

ORIGAMI_ANALYSE/origami/configOut.xml

@@ -78,12 +78,12 @@
     <param title="Import/Export parameters" gripper="False" caption="True" close_button="True" floating="True" show="False" type="mixed" />
     <param title="Linear Drift Cell" gripper="False" caption="True" close_button="True" floating="False" show="False" type="mixed" />
     <param title="Log" gripper="False" caption="True" close_button="True" floating="False" show="False" type="mixed" />
-    <param title="Multiple files" gripper="False" caption="True" close_button="True" floating="False" show="False" type="mixed" />
+    <param title="Multiple files" gripper="False" caption="True" close_button="True" floating="False" show="True" type="mixed" />
     <param title="Peak list" gripper="False" caption="True" close_button="True" floating="False" show="False" type="mixed" />
     <param title="Plot parameters" gripper="False" caption="True" close_button="True" floating="True" show="False" type="mixed" />
     <param title="Plots" gripper="False" caption="False" close_button="False" floating="False" show="True" type="mixed" />
     <param title="Processing parameters" gripper="False" caption="True" close_button="True" floating="True" show="False" type="mixed" />
-    <param title="Text files" gripper="False" caption="True" close_button="True" floating="False" show="True" type="mixed" />
+    <param title="Text files" gripper="False" caption="True" close_button="True" floating="False" show="False" type="mixed" />
     <param title="Toolbar" gripper="True" orientation="top" close_button="False" left_position="False" top_position="True" left_dockable="True" right_dockable="True" top_dockable="True" bottom_dockable="True" show="True" type="mixed" />
   </presets_gui_aui_settings>
 

ORIGAMI_ANALYSE/origami/dialogs.py

@@ -17,23 +17,24 @@
 # -------------------------------------------------------------------------
 # __author__ lukasz.g.migas
 
-# Load libraries
-import wx, itertools, os, webbrowser, wx.html
 from operator import itemgetter
-from numpy import arange, transpose, argmax, round, max, median, min, argmin
-from numpy import sum as npsum
-from wx.lib.pubsub import pub
+
+# Load libraries
+import itertools
+import os
+import webbrowser
+import wx
+import wx.html
 import wx.lib.mixins.listctrl as listmix
+from numpy import arange, transpose, argmax, min
+from numpy import sum as npsum
 
-from help import OrigamiHelp as help
-from icons import IconContainer as icons
 import plots as plots
+from help import OrigamiHelp as help
 from ids import (ID_addNewOverlayDoc, ID_helpNewVersion, ID_saveAllDocuments)
-from styles import makeCheckbox, validator, makeSuperTip, makeStaticBox, makeToggleBtn
-from toolbox import (str2num, str2int, convertRGB1to255, convertRGB255to1, num2str,
-                             isnumber, getNarrow1Ddata, dir_extra, findPeakMax, find_nearest,
-                             MidpointNormalize)
-from unidec_modules.unidectools import make_peak_shape, isolated_peak_fit
+from styles import makeCheckbox, validator, makeSuperTip
+from toolbox import (str2num, str2int, getNarrow1Ddata)
+from unidec_modules.unidectools import isolated_peak_fit
 
 
 def dlgBox(exceptionTitle="", exceptionMsg="", type="Error", exceptionPrint=True):

ORIGAMI_ANALYSE/origami/origami_requirements.txt

@@ -0,0 +1,55 @@
+attrs==19.1.0
+backports-abc==0.5
+backports.functools-lru-cache==1.5
+bokeh==0.13.0
+certifi==2019.3.9
+chardet==3.0.4
+comtypes==1.1.7
+cycler==0.10.0
+decorator==4.3.2
+enum34==1.1.6
+et-xmlfile==1.0.1
+functools32==3.2.3.post2
+futures==3.2.0
+idna==2.8
+ipython-genutils==0.2.0
+jdcal==1.4
+Jinja2==2.10
+jsonschema==3.0.1
+jupyter-core==4.4.0
+kiwisolver==1.0.1
+lxml==4.3.2
+MarkupSafe==1.1.1
+matplotlib==2.2.4
+multiplierz==2.0.14
+natsort==6.0.0
+nbformat==4.4.0
+numpy==1.16.2+mkl
+openpyxl==2.6.1
+packaging==19.0
+pandas==0.24.1
+Pillow==5.4.1
+plotly==3.7.0
+psutil==5.6.1
+pymzml==0.7.10
+pyparsing==2.3.1
+pypiwin32==223
+pyrsistent==0.14.11
+pyteomics==4.0.1
+python-dateutil==2.8.0
+pytz==2018.9
+pywin32==224
+PyYAML==3.13
+requests==2.21.0
+retrying==1.3.3
+scikit-learn==0.20.3
+scipy==1.2.1
+seaborn==0.9.0
+singledispatch==3.4.0.3
+six==1.12.0
+tornado==5.1.1
+traitlets==4.3.2
+urllib3==1.24.1
+wincertstore==0.2
+xlrd==1.2.0
+xlwt==1.3.0

ORIGAMI_ANALYSE/origami/panelExtraParameters.py

@@ -17,13 +17,15 @@
 # -------------------------------------------------------------------------
 # __author__ lukasz.g.migas
 
-import wx, os, time
+import os
+import time
+import wx
 from wx.combo import BitmapComboBox
 
-from toolbox import *
+from help import OrigamiHelp as help
 from ids import *
 from styles import layout, makeCheckbox, makeToggleBtn, makeSuperTip, makeStaticBox
-from help import OrigamiHelp as help
+from toolbox import *
 
 
 class panelParametersEdit(wx.Panel):

ORIGAMI_ANALYSE/origami/plots.py

@@ -18,37 +18,37 @@
 # __author__ lukasz.g.migas
 
 from __future__ import division, unicode_literals
+
 import itertools
-import numpy as np
+# needed to avoid annoying warnings to be printed on console
+import warnings
+from copy import deepcopy
 
 import matplotlib
+import matplotlib.cm as cm
+# import matplotlib.colors as mpl_colors
+import matplotlib.patches as patches
+import numpy as np
+from utilities.adjustText import adjust_text
 # import matplotlib as mpl
 # import matplotlib.pyplot as plt
 # from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg
 from matplotlib import gridspec
-import matplotlib.cm as cm
-# import matplotlib.colors as mpl_colors
-import matplotlib.patches as patches
-from matplotlib.ticker import MaxNLocator
 from matplotlib.collections import LineCollection
+from matplotlib.ticker import MaxNLocator
 from mpl_toolkits.axes_grid1 import make_axes_locatable
-# from mpl_toolkits.mplot3d import Axes3D
-
 from seaborn import color_palette
-from adjustText import adjust_text
-from copy import deepcopy
 
+import dialogs as dialogs
 from plottingWindow import plottingWindow
-from toolbox import (find_limits, dir_extra, determineFontColor, convertRGB1to255,
+from processing.heatmap import normalize_2D
+from processing.spectra import normalize_1D
+from toolbox import (determineFontColor, convertRGB1to255,
                      find_limits_list, MidpointNormalize, merge_two_dicts,
                      str2num, str2int, randomColorGenerator, _replace_labels,
                      remove_nan_from_list, find_limits_all)
-import dialogs as dialogs
-from processing.spectra import normalize_1D
-from processing.heatmap import normalize_2D
 
-# needed to avoid annoying warnings to be printed on console
-import warnings
+# from mpl_toolkits.mplot3d import Axes3D
 warnings.filterwarnings("ignore", category=DeprecationWarning)
 warnings.filterwarnings("ignore", category=RuntimeWarning)
 

ORIGAMI_ANALYSE/origami/unidec_modules/unidectools.py

@@ -15,7 +15,7 @@
 from scipy import signal
 from scipy import fftpack
 import matplotlib.cm as cm
-import mzMLimporter
+# import mzMLimporter
 from fitting import *
 import unidecstructure
 import tempfile
@@ -602,11 +602,11 @@ def load_mz_file(path, config=None):
 
         if extension == ".txt":
             data = np.loadtxt(path, skiprows=header_test(path))
-        elif extension == ".mzml":
-            data = mzMLimporter.mzMLimporter(path).get_data()
-            txtname = path[:-5] + ".txt"
-            np.savetxt(txtname, data)
-            print "Saved to:", txtname
+        # elif extension == ".mzml":
+        #     data = mzMLimporter.mzMLimporter(path).get_data()
+        #     txtname = path[:-5] + ".txt"
+        #     np.savetxt(txtname, data)
+        #     print "Saved to:", txtname
         elif extension.lower() == ".raw":
             data = data_reader.DataImporter(path).get_data()
             txtname = path[:-4] + ".txt"

ORIGAMI_ANALYSE/origami/utilities/__init__.py

@@ -0,0 +1 @@
+__author__ = 'Lukasz.Migas'